Entity
by isis-sg1
Summary: A chair is found in Atlantis and Sheppard just can't keep away from it.
1. Chapter 1

My first Atlantis story, read, review and enjoy 

"McKay," Sheppard sighed for the fifth time that hour. He sat knees up on the hard Atlantis floor, his head leaning against the wall. His right hand was till on his P-90 which lay comfortably on his chest, "How much longer?"

McKay waved him off, "The more you interrupt me the longer it will take."

"If you can't open that door in the next five minutes we're leaving, It's nearly lunch and I missed breakfast because of this door."

"Look, this isn't just any locked door. For some reason the Ancients made sure no-one could enter,"

"Then have you thought that maybe they had a good reason for doing that and opening that door is just going to lead to trouble?"

"Aren't you a little bit curious?"

"Every time you say that I end up in the infirmary."

McKay ignored and continued to study the crystals in the door, "I think I'm nearly there," He spoke. He typed something into his laptop and the door slid open, "Ah ha! See?"

"Stand back, We're doing this my way," Sheppard pulled himself off the floor and moved towards the doorway.

"What do you think is in there?" McKay asked incredulously.

"Maybe the Ancients locked the door because they were performing experiments of a Wraith."

"If there was a wraith in there Teyla would have been able to sense it," McKay reasoned.

"Okay okay, let's just do this slowly okay? The Ancients locked this room for a reason and I don't want you rushing in before the room's been searched properly,"

McKay took a step back and motioned for Sheppard to lead the way. He switched on the light on his P-90 and entered the dark room slowly. One by one the lights in the room turned on, bathing the large room in bright light. The octagonal room was completely empty apart from a single chair in the middle.

"A weapons chair?" McKay questioned as he walked in behind Sheppard.

"Looks like," Sheppard answered as he swept his gun over the room, "It's clear" He let his P-90 drop as he began to relax slightly.

"Why would there be two weapons chairs?"

"Double the firepower?" Sheppard asked.

"Maybe, but why hide this chair deep in the city? And why lock the room?"

Sheppard shrugged, "Maybe it was a back up chair and they didn't want it getting into the wrong hands," Sheppard stepped up onto the platform, "Is there nothing about it on the database?"

"Nothing," McKay shook his head, "Sit down."

"What?"

"Sit down, we're not going to learn anything by staring at it."

"What if its booby trapped."

"What if its booby trapped?"

"Colonel?" Weirs voice spoke from the radio, "What's going on down there?"

"The room's clear."

"We think we've found another weapons platform," McKay added.

"That's good."

"It could also be a big bomb with will detonate as soon as I sit in it," Sheppard spoke.

"I think it's worth the risk," McKay said.

"You would say that, you're no the one who has to sit in it."

"Are you scared?"

"Every time, infirmary, remember?"

"Terrified then."

Sheppard glared at McKay, "Cautious," He corrected, "Okay then….Elizabeth?"

"Yes John?"

"It would probably be a good idea to have Beckett on standby, just in case."

"Okay, be careful."

Sheppard stared at the chair for a second, sizing it up, "Okay, here it goes," He turned and slowly sat himself into the chair, "So far so good," His arms dropped onto the arm rests and he laid his head back. Nothing happened.

"Maybe it's broken," McKay began looking for the control crystals. Before McKay could find the lights in the room flickered for a second. The chair suddenly turned itself on and lurched back. McKay looked up at Sheppard, "Everything okay?" He asked. He stepped closer and noticed that Sheppard's eyes were closed, "Sheppard?"

Sheppard opened his eyes and instantly frowned, "McKay?" He called. There was no answer. Everywhere he looked was sea and sky, everyway he turned was the same. It was the Atlantis skyline but the city was missing, "Hello?" He called but no-one replied. His hands searched for his vest and gun which were missing. He looked down and found himself standing on the water. He took a tentative step forward and the rippling water held his weight, "Hello?" He called out a little louder.

"Hello?" A female voice replied.

"Hi, who am I talking to?" Sheppard replied as he searched for where the voice was coming from. A bright light appeared from the sky, almost blinding Shepard. When the light was gone Sheppard looked up, his eyes widening at the figure standing in front of him. The woman looked at him silently. Her bright turquoise eyes were the same colour as the sea and her alabaster skin made her eyes look even brighter. She had long blonde hair that fell over her shoulders in loose waves. She wore a long cobalt blue dress that fell to her bare feet. The dress was sleeveless and showed off her long delicate arms that hung loosely at her side. The V-neck exposed an expanse of pale skin that was divided by a single pendant, a cerulean stone encased in silver. Sheppard raised an eyebrow, "Hey" He smiled at the woman and she bowed, "Who are you?"

"My name is Atlantis," She answered.


	2. Chapter 2

Really glad you liked the last chapter – thanks for all the great reviews. Sorry this chapter took so long to post, I decided to re-write the chapter and then my internet didn't work!

"Atlantis?" Sheppard questioned as he took another step towards the woman. She nodded, "As in The City of Atlantis?" She nodded again, "You're named after the city?"

"No John, I am the City."

"Okay, how do you know my name and what do you mean you're the city?"

She laughed, "I am a physical representation of the city's systems. I know your name because I have watched you since the day you arrived."

"Watched?" Sheppard's eyebrows raised, "_All _the time?"

Atlantis blushed, "Yes."

"Okay well that's slightly creepy," He told her.

She cocked her head and frowned, "Why?" She asked.

"Where we come from it's very wrong to spy on people," Sheppard answered.

"I'm sorry…it's just been so long since people have lived in the city."

"You were alone for ten thousand years?"

Atlantis nodded solemnly, "Yes, I have been very lonely, It is good to have someone to talk to again."

Sheppard grinned, "You're welcome."

"I must thank you properly, for saving me from destruction by the Wraith," Atlantis walked up to Sheppard and stood only millimeters away from him.

"Really, no thanks needed." Sheppard spoke.

Atlantis leant forward and whispered in his ear, "But I must," She said and placed a lingering kiss on his cheek.

After a second Shepard regained the ability to speak, "You're v_ery_ welcome," He said. "So," He cleared his throat, "Where are we?"

"A program designed by my creators. It connects your mind to my computers."

"But why?"

"You've always had many questions John, here you have all your answers."

"Nope," Shepard shook his hea,d "I think I have more questions."

Atlantis laughed, "Ask away," She told him.

John opened his mouth to speak but stopped suddenly, "Well now I can't think of any," He frowned.

Atlantis smiled, "Many of my creators found themselves in a similar position."

"The ancients created you?"

Atlantis nodded, "I got to know every single one of them. I spent many years learning from them as they learnt from me. I don't understand it but you remind me so much of them, there is something different about you compared to the others from your world."

"Is that why you've been watching me?"

Atlantis smiled shyly, "Yes."

"Okay, well all of this is a lot to take in."

"I can imagine."

John nodded, she how absolutely no idea what it was like, "I need to brief my people about you."

"Your leader Elizabeth."

Sheppard frowned, "Yeah, you watch her too?"

"Occasionally," Atlantis answered, "She is a strong woman."

"Yes, yes she is," Sheppard looked around for an exit, "So how do I get out of here?"

"Concentrate hard on leaving and you will find yourself back in the chair room."

"Okay, I can do that."

"Will you return?"

Sheppard smiled, running his eyes over Atlantis, "I hope so," He answered.

"Good, I will look forward to your return," She nodded and before Sheppard could blink she had disappeared from sight.

Shepard closed his eyes, "There's no place like home" He said as he scrunched his eyes tightly and thought hard of the chair room. When he opened his eyes again he found Beckett and Rodney standing over him with similar worried expressions. He smiled, "Hey guys," He greeted them.

"That's all you can say? Hey guys?" Rodney cried.

"How long was I out?"

"Over fifteen minutes!" Rodney answered.

"You feeling okay lad?" Becket asked as he took Sheppard wrist to take his pulse.

"I'm feeling fine doc," He told Carson as he let the doctor do his tests.

"Well your heart rate is normal, any dizziness? Headaches?"

"Nope," Sheppard shook his head, "Can I get out of this thing now?" Becket and McKay held out a hand each. Sheppard grabbed their hands and pulled himself up.

"What happened?" McKay asked, "One minute you were being _you_ and the next I couldn't wake you."

"Elizabeth should probably hear this," Sheppard explained, "Come on."

Sheppard sat next to Elizabeth in the conference room. Filling up the rest of the chairs were the Ronon and Teyla on one side and Beckett and McKay on the other. He'd just finished telling them about the chair and was now receiving five disbelieving stares.

"You're telling me that when you sit in that chair there is a woman who claims to be the city," Elizabeth spoke first.

"She's not claiming to be the city, she is the city, its computers at least,"

"How can you be sure?"

"I just know," Sheppard answered.

"Okay, so why was the chair room so tightly locked in the first place?"

"Well think about it," McKay piped up, "If you were abandoning the city wouldn't you want to keep that room from being found? She can tell us everything we want to know, even thing that aren't in the database, that's a lot of information that would do a lot of damage if it fell into the wrong hands."

"What did you two talk about?" Teyla asked curiously.

"Oh you know, this and that," Sheppard answered cryptically, "Apparently she's been watching me," He smiled.

"Oh great," McKay rolled his eyes, "Not only do you have every woman on every planet we go to swooning after you but now you have an entire city fluttering her eyelashes at you."

"There was no fluttering of eyelashes Rodney."

"But there was something?" Teyla asked, raising an eyebrow.

"Nothing," Sheppard affirmed to the group, "Nothing happened."

"Okay, well from what you've told me it doesn't seem dangerous."

"Harmless," Sheppard spoke up.

"And Beckett found nothing wrong with you."

"He's never been healthier," Becket confirmed.

"I see no reason why you can't explore this further Colonel; you're not scheduled to go off world for another couple of days,"

"Good," He clapped his hands together, stood up and walked out the room.

"Go with him," Elizabeth told McKay. He nodded and followed Sheppard to the chair room.


	3. Chapter 3

Sheppard sat back down in the chair and instantly found himself looking at the Atlantis horizon one again.

"You came back!" An excited voice said from behind him. Sheppard spun round and found himself facing a smiling Atlantis.

"I said I would didn't I?"

"Yes you did, but you're friends looked doubtful and I was scared they would not let you come back."

John took a step forward, "You watched the briefing?" She nodded, "How?"

"There are security cameras in all of the rooms, that is how I have watched you all of this time."

Sheppard frowned, clearly confused, "Wait; there are cameras in all of the rooms? Where?"

"Hidden," Atlantis answered vaguely but with a glint in her eyes that told Sheppard she was playing with him, "Look, I will show you," She waved her hand over the water at their feet at the water turned from blue to black before displaying the chair room. Below him John could see McKay standing by the chair keeping an eye on the data from his laptop occasionally looking up to watch over himself sitting unconscious in the chair.

Sheppard crouched over the image with fascination, "That's cool… and kinda creepy" He added.

"How so?" Atlantis asked.

"I don't really spend a lot of time watching myself," Sheppard answered. It was too strange watching himself sitting in the chair and he stood back up and looked away, "Is there anyway of to use the cameras without using the chair?"

Atlantis nodded and waved the picture away, "There is a security room where all the cameras feed into. It was used by my creators to catch wrong doers. You have yet to find it"

"You going to tell me where it is?"

Atlantis laughed, "And what would be the fun in that?"

"I'm sure I'll find a way to get it out of you."

Atlantis smiled, "I hope so," Sheppard ducked his head at Atlantis' heated gaze "I'm so glad you came," Atlantis continued.

Sheppard turned his head back towards Atlantis and smiled gently, "Me too."

"It was so hard for me to just sit by and watch, waiting for you to find the chair."

"What did you do all that time?"

"While I was watching you?"

Shepard shook his head, "The ten thousand years you were alone."

Atlantis sighed as she dropped down onto the water. She leant on the water with one hand while the other dropped into the rippling water. For a brief second Sheppard wondered how that was possible before realising he was inside a computer and anything was possible. He lay down next to Atlantis, stretching his legs out in front of him and leaning on his elbows, "I slept mostly, anything else would have using up too much power."

"You must be all slept out then."

Atlantis laughed, "You are very funny."

"So I'm told."

"And modest too," Atlantis noted as she raised an eyebrow.

"Well you know Rodney has enough arrogance for the both of us."

"I have noticed, how can you stand to befriend such a man?"

"Don't be fooled, he has some redeeming qualities. Without him you probably wouldn't be here."

"All your people are very different, very emotional. My creators learnt over time to control their feelings."

"You don't like it?"

"On the contrary, it is refreshing and…entertaining."

Sheppard chuckled, "I'm glad to be of service."

Atlantis shook her head, "You are not as emotional as the others, your control reminds me of my creators. You hide many secrets."

Sheppard swallowed, "We're a complicated lot, some more than others," He explained.

"I know, you are not the only one who hides the truth."

Shepard sighed as he tried to work out how to explain this to Atlantis, "Some people, like me, have gone through things… traumatic things that we don't really like to talk about."

Atlantis bowed her head, "I understand."

"You do?"

She nodded, "The few creators that returned from battle with the wraith acted differently. I was upset to see them so distant, so unconnected from me."

"I'm sorry."

"Don't be, you are very much connected to me and that is all that matters now."

Sheppard grinned, "I was going to ask you about that."

"Yes?"

"The hum, I can feel you in my head."

Atlantis nodded in understanding, "All my creators felt the same way."

"There are other people with the gene on Atlantis, why am I the only one who can feel it?"

"It is in them also but it is so weak they can barely feel it."

"It's not just the hum though is it?" Atlantis shook her head, "You sense what I need, turn lights on, open doors, turn the heat up when I feel cold."

"The longer you stay here the stronger our bond becomes, When you first arrived I felt the gene inside you but you were still a stranger to me, over time I began to understand what you needed from me."

"It's pretty cool," John shrugged, "There are some very jealous people in the city."

Atlantis smiled, "I wish I could connect to all your people the way I do to you but most see me as nothing but buildings and computers."

"Hey," Sheppard lay a hand on her shoulder, "You are much more than that, believe me."

Atlantis blushed, "Thank you."

"Well what are friends for?"

"We are friends?" Atlantis looked up at Sheppard with wide eyes.

"Of course!" Suddenly Atlantis snapped her head away and frowned, "What is it?"

"You have been here too long; your friends are trying to disconnect you. It is dangerous to do so."

"I'll be back as soon as I can, I promise."

"I know," She nodded, "I will look forward to your return," Sheppard closed his eyes, thought hard and opened his eyes to the chair room.

"McKay," Sheppard growled.

Rodney looked up from the open crystal panel on the platform, "Your back!" He exclaimed.

"Yes, because Atlantis told me someone was messing with the chair."

"Ah yes, that was me," Sheppard gave McKay a look that said _who else? _"She also told me messing with that could have done some serious damage."

"To the chair?"

"No McKay," Sheppard stood up from the chair, "To me," He walked to the entrance and he could already feel McKay eyeing up the crystals behind him, "Stop messing with the chair," He ordered before leaving the room. He walked a couple of yards down the corridor before stopping. He turned to wall and pressed the palm of his hand against it. The hum in his head immediately became stronger and as he closed his eyes he could hear her voice calling him back to the chair.


	4. Chapter 4

McKay tucked his computer under his arm as he walked down the Atlantean corridor. He sighed as another person got in his way, "Excuse me!" He called out and the young scientist jumped out of the way.

"You know they're all completely terrified of you don't you?" McKay turned to see Elizabeth.

"Elizabeth, I didn't see you there."

"Where are you headed?" She asked as she struggled to keep up with his fast pace.

"Actually I was coming to see you," He answered.

"What can I do for you?" The pair passed through a door and entered Stargate operations.

"It's Sheppard," McKay sighed as they ascended up the stairs to the control room.

Elizabeth turned to McKay with a look of concern, "Is he okay?"

"It's been two weeks since we discovered the chair and he's spent all his free time in there."

"It's a big discovery Rodney, can you imagine how much there is to learn from it?"

"Yes, yes yes I agree but he's skipping meals and has barely slept."

Elizabeth frowned, "What does Carson have to say?"

"I came to you first, look, I think this is more than just Sheppard playing with the new toy, when he sits in that chair he's connected with this woman… representation of a woman, whatever she is."

"Are you saying Sheppard's feelings towards Atlantis are more than platonic?"

"He called her hot."

"He wouldn't get involved with her, she's just a computer programme," Weir argued.

"Any time he hasn't been in the chair she is all he's talked about. Atlantis this, Atlantis that-"

"I get the idea Rodney," She interrupted, "Okay; as soon as he's out I'll talk to him."

"Good, maybe he'll listen to you," McKay turned to leave, as an afterthought he turned back to Elizabeth, "Thank you," He told her.

Elizabeth smiled. She knew how much Rodney cared for his friend, "You're welcome," she nodded and watched silently as Rodney walked away.

"John, please take a seat," Elizabeth said as the Colonel entered her office. She hid her surprise at his appearance. There were large bags under his eyes from lack of sleep and his eyes looked distant and glassy. He'd also lost weight, she noticed.

"What's this about?" He asked wearily. He was already desperate to get back to the chair.

"It's about the chair," She began, "McKay has voiced concern that you're time in the chair is taking priority over your duties. He's also worries that you're not eating and sleeping properly. I just wanted to make sure that wasn't the case."

"I'm fine," He defended, "McKay's just being a busybody."

Elizabeth leant her arms on her desk, clasping her hands together, "How are things going with Atlantis?" She asked.

"Good, there's still a lot she can tell me though."

"And you're not…" Elizabeth struggled for the right words, "Getting too involved?"

"Involved?"

"Becoming personally attached to her."

Sheppard shook his head, "I don't understand."

"I'm just making sure you still remember that she's still a computer programme, not matter how life like she may be."

Sheppard frowned, "If you're saying what I think you're saying-"

"Just," She interrupted, "Go get something to eat, get some rest. I don't want to see you anywhere near the chair for at least a day."

Sheppard sighed, "Fine," He growled before he stood up and left the room.

He stopped off at the mess hall first and picked up a plate of food. He moved to an empty table, ignoring requests from soldiers to sit with them. He picked up his fork and picked at the sloppy food with little interest in eating it. He dumped the food and stalked to his quarters. He thought about doing some work on his laptop but that wasn't appealing either. He pulled off his boots and took his radio off his ear and climbed into bed. Without doing anything the lights in his room turned off the lights and the shutters over the windows closed leaving him in darkness, "Thank you Atlantis," He called out to the room before closing him eyes. He tossed and turned for an hour as he tried to sleep but the humming in the back of his head had intensified and was keeping him awake. Atlantis obviously wanted to see him again. He opened his eyes and sighed, "Screw this," He threw back the covers and the lights turned back on. He quickly tied his boots on but left his radio on his bedside table as he left the room. He moved silently through the halls towards the chair room, hiding in rooms to avoid bumping into anyone. It wasn't long before he walked into the chair room. He stopped when he saw Beckett sitting in the chair.

"Carson?" He called.

The chair lifted back into its upright position and Carson looked at him, "Colonel," He greeted, "I'd thought I'd see what you were raving about but I can't seem to get it to work."

"Guess it only likes me," He answered.

Beckett frowned, "I thought Elizabeth told you to stay away from the chair?" He asked as he pulled himself up.

"She told me to get some rest and I did," Sheppard twisted the truth. Beckett didn't look convinced, "Look if you're so concerned why don't stay here and monitor me."

"Aye, I will," He answered with a raised eyebrow. Sheppard smiled slight and moved towards the chair, already feeling the humming decreasing as he neared the chair. He sat down in the chair and smiled even more when he came face to face with Atlantis.

"You were gone for so long," She spoke, "I was worried."

"It was only a couple of hours," Sheppard reassured, placing a comforting hand on her arm, "I came back as soon as I could."

She stared at the ocean beneath their feet, "If you did not want to see me you should have just said so."

"Of course I wanted to see you!" Sheppard cried, "Why wouldn't I?"

"Your leader," She shrugged, "I've seen the way you look at each other."

"Atlantis trust me," He pulled her into a hug, "I want to be here," He told her. Suddenly she stiffened in his arms and pulled herself away, "What is it?" He asked.

"A Wraith Hive ship," McKay turned to Elizabeth, "It just popped up on the sensors."

"How long before it gets here?" She grimaced.

"A couple of days, maybe less," McKay sighed and turned back to the screen showing the glowing shape of the Hive as it slowly made its way to the larger glowing dot indicating Atlantis.

"Okay, let's hope they still think the city has been destroyed. Raise the cloak just before they arrive but get ready to switch to the shield on my order," McKay nodded. "We'll also evacuate all non essential personnel," She added.

"It's a Wraith Hive shi,p" Atlantis explained as she took a step back, "It's on its way here."

"What? How long?"

"A day, maybe two," She answered, "It is not safe anymore."

"That's not true," He shook his head firmly, "We have the cloak, if that doesn't work we can always switch to the shield. I can use the drone chair to blow it out of the sky."

"You could get hurt."

"The chances of that happening are remote," He assured her, "I've survived before, I'll get through this one alive, I promise."

"I can't take that chance," She told him.

"What do you mean?" He took a step towards her but she took another step back.

"You have to stay here," She explained.

"I can't, I have to go and protect my people."

"I'm sorry John, I can't let you go," Sheppard cried as he felt electric course through his body. As it left him he dropped to the floor.

"What the hell was that!" He shouted.

"I'm sorry," She shook her head but didn't explain. He closed his eyes and concentrated hard on the chair room but nothing happened. He tried again but again he opened his eyes to Atlantis. No matter what he tried he couldn't leave.

"What have you done?"

Beckett watched in horror as Sheppard body convulsed in the chair.

"Medical team to the chair room!" He shouted into his radio. As the convulsions subsided he stepped onto the chair platform and leant over Sheppard. He took a pulse, it was weak but it was there. He leant closer and realised he wasn't breathing. "Hurry!" He called as he began breathing for the Colonel.


	5. Chapter 5

I'm not too happy with this chapter so I hope you like it (Now you might understand why the story's called Entity – think back to a certain SG episode)

Ronon, Teyla, McKay and Elizabeth sat outside the infirmary with similar worried expressions. They'd heard over the radio that something had happened to Sheppard and had rushed to the infirmary but Beckett wasn't finished examining Sheppard so they were still left in the dark, not knowing whether Sheppard was just simply unconscious or something serious was wrong with him.

"This is all my fault," McKay sighed as he walked back and forth in the small corridor outside the infirmary.

"Why is that?" Teyla looked up at her pacing team-mate.

"I should have been watching him more closely, stopped him from going back in that damn chair."

"You couldn't have known," Elizabeth said with a sigh, "I however should have known he wouldn't… he couldn't stay away from it."

"Blame does no one any good," Teyla said.

Elizabeth sighed again, "You're right, it doesn't matter whose fault it is and we both tried to help him. If only he had listened. I still can't shed that image of him in my office. His eyes glassed over, his uniform hanging off him, the chair was a drug and we let him become an addict."

"This couldn't have come at a worse time," McKay exclaimed.

"Rodney!" Teyla exclaimed.

"If Sheppard is seriously injured then there isn't anyone to control the drone chair," Rodney argued his point.

"Carson has used it on occasion," Elizabeth spoke up,

"Yes, he's managed to get it working but he hyperventilates anytime he has to get near the thing and he can barely stop the drones from crashing into the city. He doesn't have enough control to destroy a Wraith dart let alone a hive ship."

"He's got a point," Ronon growled.

"There's no point in speculation until we know the Colonel's condition," Elizabeth said, "And anyway, using the drone chair is only a last resort. Even if, _if-"_ She emphasised, "-he is seriously injured, we might not even need to sue the drone chair."

"Let us all think positively," Teyla said.

"Yes because that'll work," McKay snapped.

"Rodney!" Elizabeth chided.

He sighed, "I'm sorry, I'm just…fed up of waiting outside the infirmary waiting for news on Sheppard."

"Unfortunately this happens too often," Teyla agreed.

"What do you wanna do? Lock him up to stop him from getting hurt?" Ronon asked. Everyone knew they couldn't stop him going off world and no one could stop him from getting into trouble. "He's a soldier, a grown man, you're not going to stop him from doing anything he wants to do or stop him from doing what it takes to protect this place," Elizabeth closed her eyes, remembering the look in his eyes before he left on the suicide mission and the many times she nearly lost him. Her thoughts were interrupted when Carson exited the infirmary. Her heart dropped when she saw the look on his face. She stood up, as did Ronon and Teyla.

"Carson?" She asked, "How is he?"

Carson shook his head before forcing himself to look Elizabeth in the eye, "Not good."

"What does not good mean?" Ronon asked with a frown. He was useless in situations like this. Medical jargon meant nothing to him.

"While in the chair he suffered some sort of convulsive attack, we got him to the infirmary as soon as possible but I'm afraid the damage had already been done."

"Carson, please," Elizabeth pleaded. She needed to know.

He sighed, "Come, I'll show you." He lead them into the infirmary and Elizabeth gasped as she saw all the tubes and wires. "He wasn't breathing. We put him on a ventilator to keep him breathing. His heart had also stopped; those machines are keeping his heart beating."

Elizabeth shook her head, "That's not good."

"No, it's not. I did an EEG but unfortunately I found no brain activity,"

"I don't understand," Ronon said with a frown. It was hard to look at his friend looking so weak and helpless.

"I'm afraid he's brain dead. All that equipment is keeping him alive."

"That's definitely not good," McKay slumped into the nearest chair and placed his head in his hands.

"What can you do for him?" Teyla asked.

"I'm sorry lass; there is nothing I can do. The life support can keep him alive but his brain is dead, if I turn the machines off he'll stop breathing, then his heart will stop. I don't know what the chair did to him but the damage is beyond repair. I'm sorry,"

Elizabeth couldn't believe what Carson was saying. She pulled a spare chair towards Sheppard's bed and sat down in it, taking Sheppard's limp cold hand in her own. She watched the ventilator inflate and deflate his lungs and listened to the whirrs and beeps on the machines keeping his heart beating.

Carson moved to stand behind her, "I'm so sorry lass," He spoke softly, "I know how much you care for him."

Elizabeth swallowed hard, "Thank you."

"There is something we have to talk about," Carson started tentatively, "How long we should keep him on life support. He wouldn't want to live like this."

"I can't…not yet," She shook her head.

Carson laid a comforting hand on her shoulder and squeezed, "I understand," He stayed there watching over his patient and his friends as they took in the information he'd just presented them with.


	6. Chapter 6

I know I promised this a long time ago but I was having problems with this chapter and had no idea where I was going to go with it. So I hope you like it.

Sheppard closed his eyes, trying with all his might to escape but again nothing happened. He opened his eyes and glared at Atlantis.

"What have you done?" He growled. She took a step back and shook her head but said nothing, "What have you done?!" He shouted.

"I had to," She whispered, "To protect you."

"Let me out," He ordered forcefully. The kind of voice he used on his men.

"I can't," She stood her ground.

"Let me out of here!"

"I can't!" She repeated, shaking her head, "It is impossible."

"Why?" He took a step forward. She waved her hand over the water and the view of the chair room appeared. His eyes widened at the empty chair, "Where am I?" She waved her hand again and this time to a view of the infirmary. His body was lying in one of the beds, attached to various machines and his team sat around him. He crouched over image and reached out. He closed his eyes as the image faded away and his hand clenched, "Why is my body in the infirmary?"

"Your Doctor brought you there after the transplantation."

He shook his head in confusion, "Transplantation?" He questioned.

"When you sit in the chair your mind is temporarily connected to the computers. I have transplanted your consciousness into the computer….permanently."

"You did what?"

"You're mind can only be transplanted back if your body is in the chair and your friends believe you to be beyond help."

"I didn't ask for this!"

"Why can't you accept what I have done?"

"Because I don't belong here Atlantis. I'm needed out there!"

"I need you more!"

John stopped; he looked up at her, "What?" He asked softly as he slowly rose to his feet.

"We can be together now," She smiled and placed a hand on his arm.

He stepped away from her, "Atlantis," He said with a sigh, "I like you, I really do."

"But?"

"I like you as a friend Atlantis."

She shook her head, "I don't understand."

"I'm sorry, but I don't feel the same way. I thought you knew that."

She turned away from him. He took a step towards her, "I'm sorry," He placed a hand on her shoulder.

She shrugged him off, "Get away from me!" She cried.

"Atlantis, please."

"Leave me alone," She began to run.

"Atlantis wait!" He shouted.

"No!" She shouted back. She disappeared and Sheppard sunk to the ground. He dropped his head into his hands and breathed loudly.

"Atlantis," He said softly, "I know you can hear me……I'm sorry, I really am. But you have to let me go. My people need me, The Wraith are coming and I have to protect them, protect _you_ from being destroyed." He received no answer, just the soft crying.

"I still want to be your friend Atlantis, I'll still visit, there's still so much we could learn from each other, but I have to go, I have to find a way out of here." He slumped back, lying over the water and watched the clouds in the sky. There was no wind, no smell of sea salt, no heat from the sun. He didn't know how he could ever stay there. He twisted onto his side and looked down at the rippling water and wished that he could sea his friends. His eyes widened as his wish was fulfilled and the water turned black and then back to the view of the infirmary where they were sitting at his bedside. He thought only Atlantis could manipulate the water. He concentrated and wished he could hear their voices.

"_I'm so sorry lass,"_ Sheppard recognised the Scottish accent, _"I know how much you care for him."_

Sheppard swallowed hard, _"Thank you."_

"_There is something we have to talk about, How long we should keep him on life support. He wouldn't want to live like this." _No! Sheppard thought. If they took him off life support then he would be stuck in the computers forever with no chance of getting back.

"_I can't…not yet,"_ He watched her shake her head and smiled. Thank god for Elizabeth, he thought. She'd just given him the chance he needed. If only he had a way of communicating with them. He frowned. If he could watch and listen to them, what else could he do. He thought about turning the lights on and off in the infirmary where his team was but wasn't going to risk it in case he accidentally turned the life support off instead.

A light bulb went off in his head and he thought about the Atlantian screen in Stargate operations. He pictured it in his head and typed a message. The water underneath him showed the message he was writing and he frowned at the Ancient symbols. Damn, the message was all in Ancient. Now he would have to wait until it was translated.

"Dr Weir?"

"Yes Chuck?" Elizabeth sighed into her radio.

"I'm sorry to disturb you but the screen's just popped up with a bunch of Ancient writing, I've already had Dr French to translate it."

Elizabeth frowned and tilted her head to one side, "What does it say?"

"In out, in out-"

"What is it? The lyrics to the hokey pokey?" McKay interrupted as he listened inover his own radio. Elizabeth sent him a glare.

Chuck continued, "Body outside, inside knowledge, Atlantis."

"That's all?"

"Yes Ma'am."

"Okay," He rubbed her temples, feeling a headache coming on. Her military commander and friend was currently being kept alive by machines and the last thing she needed was Atlantis sending cryptic messages. "Contact me if it happens again," She switched off and turned back to watch Sheppard sleep.

Sheppard sighed and mentally kicked himself. Of course his message wasn't going to translate word for word, The ancient language was a complicated one, one he'd never bothered to learn. Now he had to find another way to communicate with them.


	7. Chapter 7

Yep, it's taken me ages again! Hope this chapter makes up for it (And I hope it makes sense I write it quite quickly!) Please read and review :)

* * *

John stared gloomily at the image of his friends sitting at his bedside. His first idea to get their attention had failed miserably and he didn't know what to do next.

Ronon was standing against the wall of the infirmary, his arms crossed tightly across his chest. He watched over John's body silently whilst McKay sat on one of the spare beds, busying himself with his laptop and occasionally bickering with Radek over his radio. Every now and again he would look up, as if he was checking John was still there, before looking back down at his computer. Teyla was sitting on his left, reading quietly from a book whilst Elizabeth sat on his right, her hand holding his tightly. He watched them well into the night as one by one they left to their own rooms to sleep until only Elizabeth was left.

"Elizabeth?" John watched as Carson entered the room. She lifted her head wearily and smiled weakly at Carson, "It's late lass you should be in bed."

"I'm fine."

Carson took another step forward and looked at Elizabeth with sympathy, "He wouldn't want this."

She sighed, "I know, you've told me."

"I'm talking about you; The last thing he'd want is you sitting at his bedside, putting him before your welfare, get some sleep lass."

Elizabeth nodded reluctantly, "I will," She promised. Carson smiled before walking away. Elizabeth turned back to John.

"Tell me what to do," She whispered, "Give me a sign John because I don't know what to do," She placed a single kiss on his forehead and let go of his hand, letting it drop back onto the bed. She took one last look at his unmoving form before quietly slipping out of the room.

"I'm trying Elizabeth," John said to himself, wishing she could hear. Suddenly an idea came to him. It was perfect yet so simple. He just wished he didn't have to wait until the morning. He was desperate to be back in his body, laughing with his team in the mess till the early hours, running with Ronon, sparring with Teyla, bickering with Rodney and flirting with Elizabeth.

* * *

The next morning Elizabeth took the work she'd been neglecting and a large mug of coffee and returned to her place by John's bedside. There was still no change but she wasn't expecting one. She knew there was no chance of recovery. As soon as she was sat down she was called over the radio.

"Dr Weir?"

"Yes Chuck?"

"The power's gone out, all over the city."

"What?" She frowned as she scanned her eyes over the fully lit infirmary, "Are you sure, the power's still on here."

"Yes Ma'am, The city's only powering three rooms, Stargate operations, the infirmary and the second chair room."

"Those are the only rooms powered up?"

"We've been trying everything Elizabeth but I jut can't seem to- Elizabeth heard McKay interject and then stop mid sentence.

"Rodney?"

"Yes, yes, yes, just a second," McKay snapped.

"Rodney!" Elizabeth called again after no response.

"For some reason the city's gone into a lockdown."

"Why?"

"Did I not just say I didn't know the reason why?"

She ignored him, "How long till it's fixed?"

"Just a minute," Rodney spoke up distractedly.

"What's going on?" Carson asked.

"The city's acting up," She explained, snapping her head round to greet the doctor.

"Of course," Beckett rolled his eyes.

"Rodney!" Elizabeth called impatiently.

"Some of the doors are still open."

"A malfunction?"

"I don't think so; it's not a co-incidence that all the open doors lead from the infirmary to the second chair room."

Elizabeth frowned again, "What?"

"Do I stutter?" Rodney asked.

Elizabeth looked at Carson and saw her confusion reflected in his eyes, "Why would the city do this?" Carson asked.

Elizabeth's eyes widened and her head slowly rotated until her eyes fell upon John, "No," She shook her head, "It can't be."

"What is it?"

"It's John," She spoke, barely believing what she was saying.

"How is John doing all of this?" Carson asked.

"You said he's brain dead right?" Carson nodded, having no idea where Elizabeth was going with this, "You said his body convulsed."

"Yes," He sounded slowly, raising an eyebrow in Elizabeth's direction.

"So what if- and I know this sounds crazy but, what if his brain, his consciousness was somehow downloaded into the city's computers."

"Elizabeth-

"Think about it!" She interrupted. She rose from her chair, "The only doors open lead straight from here to the chair room which is powered up ready…he's trying to send us a message. He wants to go back in the chair!"

"I really don't see how that's possible," He shook his head.

She ignored him, "John!" She shouted, "If you can hear me… flicker the lights," Elizabeth waited and a moment later the lights in the infirmary turned off for a second then flickered slightly before they came back on. She laughed, "See?"

"Well I never," Carson couldn't believe what he was seeing.

"Are you in the computer?" She shouted and the lights flickered again, "Do you need to go back in the chair?" The lights flickered furiously that time and Elizabeth laughed again, "I think that's a definite yes."

"What's going on down there?" Rodney called through the radio.

"We're putting John back in the chair," She answered as she watched Carson get to work. He exchanged John's heart monitor for a portable one and then took him off the vent, switching it quickly with a bag.

"Come on," He pushed air into John's lungs manually as the pair pushed the gurney down the empty corridors towards the chair room. Between the two of them they were able to get him back in the chair.

"Elizabeth, Carson, the city's back online," Rodney informed them through the radio.

"Then get down here," Elizabeth replied as she watched Cason continue to bag John.

"Now what?" Carson asked.

Elizabeth shook her head, "I don't know."


End file.
